diff --git a/Cantera/matlab/cantera/private/ctfunctions.cpp b/Cantera/matlab/cantera/private/ctfunctions.cpp
index ce1ee5971..f6b937e22 100644
--- a/Cantera/matlab/cantera/private/ctfunctions.cpp
+++ b/Cantera/matlab/cantera/private/ctfunctions.cpp
@@ -1,3 +1,9 @@
+/**
+ *   @file ctfunctions.cpp
+ */
+/*
+ *  $Id$
+ */
 
 #include "mex.h"
 #include "../../../clib/src/ct.h"
@@ -22,11 +28,8 @@ void ctfunctions( int nlhs, mxArray *plhs[],
     int nrhs, const mxArray *prhs[] )
 {
     int job = getInt(prhs[1]);
-        
-    int j, m, iok, id, dbg, validate;
-    char *file, *key, *val;
-
-    char *infile, *dbfile, *trfile, *outfile, *idtag;
+    int iok, dbg, validate;
+    char *infile, *dbfile, *trfile, *idtag;
     int buflen;
     char* output_buf;
 
diff --git a/Cantera/matlab/cantera/private/ctmethods.cpp b/Cantera/matlab/cantera/private/ctmethods.cpp
index f21e68981..37082547c 100644
--- a/Cantera/matlab/cantera/private/ctmethods.cpp
+++ b/Cantera/matlab/cantera/private/ctmethods.cpp
@@ -10,6 +10,10 @@
  */
 
 #include "../../../clib/src/ct.h"
+#include <string>
+//#include "../../../src/base/ct_defs.h"
+//#include "../../../src/base/global.h"
+//#include "../../../src/base/logger.h"
 #include "mex.h"
 #include "ctmatutils.h"
 #include "mllogger.h"
@@ -76,7 +80,9 @@ static Cantera::ML_Logger* _logger = 0;
 void initLogger() {
     if (!_logger) {
         _logger = new Cantera::ML_Logger;
-        setLogWriter(_logger);
+        // Call the DLL program to set the logger
+        void * vl = (void *) _logger;
+        int retn = setLogWriter(vl);
     }
 }
 
@@ -86,7 +92,8 @@ extern "C" {
     void mexFunction( int nlhs, mxArray *plhs[],
         int nrhs, const mxArray *prhs[] )
     {
-
+        // mexPrintf("Number of lhs = %d\n", nlhs);
+        // mexPrintf("number of rhs = %d\n", nrhs);
         // create a log writer for error messages if this is the
         // first MATLAB function call
         initLogger();      
diff --git a/Cantera/matlab/cantera/private/flowdevicemethods.cpp b/Cantera/matlab/cantera/private/flowdevicemethods.cpp
index 09d15edeb..d46e3abfc 100644
--- a/Cantera/matlab/cantera/private/flowdevicemethods.cpp
+++ b/Cantera/matlab/cantera/private/flowdevicemethods.cpp
@@ -10,9 +10,7 @@
     void flowdevicemethods( int nlhs, mxArray *plhs[],
         int nrhs, const mxArray *prhs[] )
     {
-        int j, m, iok, n;
-        char *file, *key, *val;
-
+        int m, iok, n;
         int job = getInt(prhs[1]);
         int i = getInt(prhs[2]);
 
diff --git a/Cantera/matlab/cantera/private/mixturemethods.cpp b/Cantera/matlab/cantera/private/mixturemethods.cpp
index a5a91c35d..fc0018012 100644
--- a/Cantera/matlab/cantera/private/mixturemethods.cpp
+++ b/Cantera/matlab/cantera/private/mixturemethods.cpp
@@ -1,4 +1,9 @@
-
+/**
+ * @file mixturemethods.cpp
+ */
+/*
+ *    $Id$
+ */
 #include "mex.h"
 #include "../../../clib/src/ctmultiphase.h"
 #include "../../../clib/src/ct.h"
@@ -9,9 +14,7 @@ using namespace std;
     void mixturemethods( int nlhs, mxArray *plhs[],
         int nrhs, const mxArray *prhs[] )
     {
-        int j, m, iok, n;
-        char *file, *key, *val;
-
+        int m, iok, n;
         int job = getInt(prhs[1]);
         int i = getInt(prhs[2]);
 
diff --git a/Cantera/matlab/cantera/private/mllogger.h b/Cantera/matlab/cantera/private/mllogger.h
index 51d90e1df..30d0e2dd3 100644
--- a/Cantera/matlab/cantera/private/mllogger.h
+++ b/Cantera/matlab/cantera/private/mllogger.h
@@ -1,3 +1,10 @@
+/**
+ * @file mlloger.h
+ */
+/*
+ * $Id$
+ */
+
 #ifndef MLLOGGER_H
 #define MLLOGGER_H
 
@@ -6,9 +13,9 @@
 #include "cantera/kernel/logger.h"
 
 #include <iostream>
-using namespace std;
+//using namespace std;
 
-static string ss = "disp(' ";
+static std::string ss = "disp(' ";
 
 namespace Cantera {
 
@@ -18,7 +25,7 @@ namespace Cantera {
         virtual ~ML_Logger() {}
 
 
-        virtual void write(const string& s) {
+		virtual void write(const std::string& s) {
             char ch = s[0];
             int n = 0;
             while (ch != '\0') {
@@ -36,10 +43,14 @@ namespace Cantera {
             }
         }
 
+        virtual void writeendl(const std::string& msg) {
+           mexPrintf("\n");
+        }
 
-        virtual void error(const string& msg) {
-            string err = "error("+msg+");";
-            mexEvalString(err.c_str());
+		virtual void error(const std::string& msg) {
+			std::string err = "error("+msg+");";
+            //mexEvalString(err.c_str());
+            mexErrMsgTxt(err.c_str());
         }
 
         virtual int env() {
diff --git a/Cantera/matlab/cantera/private/onedimmethods.cpp b/Cantera/matlab/cantera/private/onedimmethods.cpp
index af60b8a24..b284260ff 100644
--- a/Cantera/matlab/cantera/private/onedimmethods.cpp
+++ b/Cantera/matlab/cantera/private/onedimmethods.cpp
@@ -218,7 +218,7 @@ void onedimmethods( int nlhs, mxArray *plhs[],
         double lower, upper, rtol, atol, *grid, *pos, *values, 
             mdot, t, p, val, *temp, ratio, slope, curve, tstep, *dts, 
             rdt, prune;
-        int nlower, nupper, nr, na, npts, np, nv, comp, localPoint, idom,
+        int npts, np, nv, comp, localPoint, idom,
             loglevel, refine_grid, n, flag, itime, ns, *nsteps, icount,
             onoff, ss_age, ts_age;
         char *xstr, *fname, *id, *desc, *name;
diff --git a/Cantera/matlab/cantera/private/phasemethods.cpp b/Cantera/matlab/cantera/private/phasemethods.cpp
index 1ebfdc6f8..3a958f1df 100644
--- a/Cantera/matlab/cantera/private/phasemethods.cpp
+++ b/Cantera/matlab/cantera/private/phasemethods.cpp
@@ -1,3 +1,9 @@
+/**
+ *  @file phasemethods.cpp
+ */
+/*
+ *  $Id$
+ */
 
 #include "mex.h"
 #include "ctmatutils.h"
@@ -12,7 +18,6 @@
         int job = getInt(prhs[2]);
             
         bool ok = true;
-        int status, buflen;
         char* input_buf;
         double* ptr = 0;
         int n, nsp, mjob, show_thermo;
diff --git a/Cantera/matlab/cantera/private/reactormethods.cpp b/Cantera/matlab/cantera/private/reactormethods.cpp
index b1000b1bd..49bad594c 100644
--- a/Cantera/matlab/cantera/private/reactormethods.cpp
+++ b/Cantera/matlab/cantera/private/reactormethods.cpp
@@ -1,3 +1,9 @@
+/**
+ * @file reactormethods.cpp
+ */
+/*
+ *  $Id$
+ */
 
 #include "mex.h"
 #include "../../../clib/src/ctreactor.h"
@@ -7,8 +13,7 @@
     void reactormethods( int nlhs, mxArray *plhs[],
         int nrhs, const mxArray *prhs[] )
     {
-        int j, m, iok, n;
-        char *file, *key, *val;
+        int iok, n;
 
         int job = getInt(prhs[1]);
         int i = getInt(prhs[2]);
diff --git a/Cantera/matlab/cantera/private/reactornetmethods.cpp b/Cantera/matlab/cantera/private/reactornetmethods.cpp
index c45494003..766ae885f 100644
--- a/Cantera/matlab/cantera/private/reactornetmethods.cpp
+++ b/Cantera/matlab/cantera/private/reactornetmethods.cpp
@@ -1,3 +1,9 @@
+/**
+ * @file reactornetmethods.cpp
+ */
+/*
+ *   $Id$
+ */
 
 #include "mex.h"
 #include "../../../clib/src/ctreactor.h"
@@ -9,9 +15,7 @@
     void reactornetmethods( int nlhs, mxArray *plhs[],
         int nrhs, const mxArray *prhs[] )
     {
-        int j, m, iok, n;
-        char *file, *key, *val;
-
+        int iok, n;
         int job = getInt(prhs[1]);
         int i = getInt(prhs[2]);
 
diff --git a/Cantera/matlab/cantera/private/thermomethods.cpp b/Cantera/matlab/cantera/private/thermomethods.cpp
index 2ab22d819..02286ed88 100644
--- a/Cantera/matlab/cantera/private/thermomethods.cpp
+++ b/Cantera/matlab/cantera/private/thermomethods.cpp
@@ -1,4 +1,9 @@
-
+/**
+ *  @file thermomethods.cpp
+ */
+/*
+ * $Id$
+ */
 #include "mex.h"
 #include "../../../clib/src/ct.h"
 #include "ctmatutils.h"
@@ -10,7 +15,6 @@ static void thermoset( int nlhs, mxArray *plhs[],
     //    mexErrMsgTxt("wrong number of input parameters.");
     //}
     int ierr = 0;
-    double vv;
     int th = getInt(prhs[1]);
     int job = -getInt(prhs[2]);
     double* ptr = 0;
diff --git a/Cantera/matlab/cantera/private/wallmethods.cpp b/Cantera/matlab/cantera/private/wallmethods.cpp
index d705428d9..1b7cf7e20 100644
--- a/Cantera/matlab/cantera/private/wallmethods.cpp
+++ b/Cantera/matlab/cantera/private/wallmethods.cpp
@@ -1,4 +1,9 @@
-
+/**
+ *  @file wallmethods.cpp
+ */
+/*
+ *   $Id$
+ */
 #include "mex.h"
 #include "../../../clib/src/ctreactor.h"
 #include "../../../clib/src/ct.h"
@@ -9,9 +14,7 @@
     void wallmethods( int nlhs, mxArray *plhs[],
         int nrhs, const mxArray *prhs[] )
     {
-        int j, m, iok, n;
-        char *file, *key, *val;
-
+        int m, iok, n;
         int job = getInt(prhs[1]);
         int i = getInt(prhs[2]);
 
diff --git a/Cantera/matlab/cantera/private/xmlmethods.cpp b/Cantera/matlab/cantera/private/xmlmethods.cpp
index 97ea8aadb..00397e429 100644
--- a/Cantera/matlab/cantera/private/xmlmethods.cpp
+++ b/Cantera/matlab/cantera/private/xmlmethods.cpp
@@ -1,3 +1,9 @@
+/**
+ *  @file xmlmethods.cpp
+ */
+/*
+ *  $Id$
+ */
 
 #include "mex.h"
 #include "../../../clib/src/ctxml.h"
@@ -23,7 +29,7 @@ static bool nargs_ok(int job, int n) {
 void xmlmethods( int nlhs, mxArray *plhs[],
     int nrhs, const mxArray *prhs[] )
 {
-    int j, m, iok, id;
+    int j, m, iok;
     char *file, *key, *val, *nm;
 
     int job = getInt(prhs[1]);